Well, I tried spidering another site on the server and phpDig was recognized as the user-agent in the logs.
Being a little perplexed I wrote a quick script with apache_request_headers() and ran it on the site that hasn't been recognizing phpDig. There appears to be a "ghost" cookie being sent that isn't being picked up and echoed back to the server. It's a phpbb2mysql_data cookie. I'm not even sure why it's being set on that site since phpbb hasn't been on that site...ever.
Now I don't even know where to start looking for that to fix it.
User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.7.5) Gecko/20041107 Firefox/1.0
Accept: text/xml,application/xml,application/xhtml+xml,text/html;q=0.9,text/plain;q=0.8,image/png,*/*;q=0.5
Accept-Language: en-us,en;q=0.5
Accept-Encoding: gzip,deflate
Accept-Charset: ISO-8859-1,utf-8;q=0.7,*;q=0.7
Keep-Alive: 300
Cookie: lang=english; phpbb2mysql_data=s%3A0%3A%22%22%3B; osCsid=%cookie deleted%
The osCsid is being echoed back by phpDig, the phpbb2 is not.